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- PDB-3hkm: Crystal Structure of rice(Oryza sativa) Rrp46 -

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Basic information

Entry
Database: PDB / ID: 3hkm
TitleCrystal Structure of rice(Oryza sativa) Rrp46
ComponentsOs03g0854200 protein
KeywordsHYDROLASE / RNase PH domain / PHOSPHORYLASE
Function / homology
Function and homology information


cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / : / DNA nuclease activity / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / rRNA catabolic process / nuclear mRNA surveillance / exonuclease activity / RNA nuclease activity ...cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / : / DNA nuclease activity / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / rRNA catabolic process / nuclear mRNA surveillance / exonuclease activity / RNA nuclease activity / rRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double-stranded DNA binding / single-stranded RNA binding / nucleolus / identical protein binding
Similarity search - Function
GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Exosome complex exonuclease RRP46 homolog
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9845 Å
AuthorsYang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Yuan, H.S.
CitationJournal: Rna / Year: 2010
Title: Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation
Authors: Yang, C.-C. / Wang, Y.-T. / Hsiao, Y.-Y. / Doudeva, L.G. / Kuo, P.-H. / Chow, S.Y. / Yuan, H.S.
History
DepositionMay 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Os03g0854200 protein
B: Os03g0854200 protein
C: Os03g0854200 protein


Theoretical massNumber of molelcules
Total (without water)81,0383
Polymers81,0383
Non-polymers00
Water7,494416
1
A: Os03g0854200 protein


Theoretical massNumber of molelcules
Total (without water)27,0131
Polymers27,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Os03g0854200 protein


Theoretical massNumber of molelcules
Total (without water)27,0131
Polymers27,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Os03g0854200 protein


Theoretical massNumber of molelcules
Total (without water)27,0131
Polymers27,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.607, 111.607, 57.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsDIMER DISSOCIATED INTO MONOMERS IN REMARK 350 THE CRYSTALLIZATION CONDITION

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Components

#1: Protein Os03g0854200 protein / Rrp46 / cDNA clone:J023009H04 / full insert sequence / 3' exoribonuclease family / domain 1 ...Rrp46 / cDNA clone:J023009H04 / full insert sequence / 3' exoribonuclease family / domain 1 containing protein / expressed / Putative exosome component


Mass: 27012.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Strain: Japonica Group / Gene: putative exonuclease RRP46 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIPL)
References: UniProt: Q84T68, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Description: The original data was scaled to 2.0 Angstrom by HKL2000. Then refinement was performed with all scaled data automatically by phenix.refine. The highest resolution of 1.98A was made by phenix.refine.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2008
RadiationMonochromator: Si 111 chnnel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.501
ReflectionResolution: 1.98→50 Å / Num. obs: 55506 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Rmerge(I) obs: 0.057 / Rsym value: 0.065 / Net I/σ(I): 21.65 / Num. measured all: 185470
Reflection shellResolution: 1.98→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.15 / Num. unique all: 5536 / Rsym value: 0.354 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NN6 chain D

2nn6


Resolution: 1.9845→26.807 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.835 / Isotropic thermal model: isotropic / σ(F): 0.12 / Phase error: 24.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 2776 5.07 %random
Rwork0.1694 52028 --
obs0.1727 54782 98.55 %-
all-55487 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.857 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 45.5 Å2 / Biso mean: 26.089 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.148 Å20 Å2-0 Å2
2--0.148 Å2-0 Å2
3----0.297 Å2
Refinement stepCycle: LAST / Resolution: 1.9845→26.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 0 416 5102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064763
X-RAY DIFFRACTIONf_angle_d1.096443
X-RAY DIFFRACTIONf_dihedral_angle_d18.4151763
X-RAY DIFFRACTIONf_chiral_restr0.072752
X-RAY DIFFRACTIONf_plane_restr0.006831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9845-2.01870.27651270.23012413X-RAY DIFFRACTION98
2.0187-2.05540.3321320.23492525X-RAY DIFFRACTION98
2.0554-2.09490.25881390.22532590X-RAY DIFFRACTION98
2.0949-2.13760.2691460.21192562X-RAY DIFFRACTION98
2.1376-2.18410.2311320.20852520X-RAY DIFFRACTION98
2.1841-2.23490.24281380.20692646X-RAY DIFFRACTION98
2.2349-2.29070.24361350.20672593X-RAY DIFFRACTION98
2.2907-2.35260.29791400.20242589X-RAY DIFFRACTION98
2.3526-2.42180.25261430.20352659X-RAY DIFFRACTION98
2.4218-2.49990.26651420.19382605X-RAY DIFFRACTION98
2.4999-2.58920.24661420.19552627X-RAY DIFFRACTION98
2.5892-2.69280.31661370.18932605X-RAY DIFFRACTION98
2.6928-2.81520.2091400.18522634X-RAY DIFFRACTION98
2.8152-2.96340.24081480.18222612X-RAY DIFFRACTION98
2.9634-3.14890.23141380.17292666X-RAY DIFFRACTION98
3.1489-3.39150.20321380.14912654X-RAY DIFFRACTION98
3.3915-3.7320.18981310.13792623X-RAY DIFFRACTION98
3.732-4.27020.20631250.12272641X-RAY DIFFRACTION98
4.2702-5.37290.22921440.12612643X-RAY DIFFRACTION98
5.3729-26.80960.21251370.16442621X-RAY DIFFRACTION98

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